1am2 - Revision history

OCA at 06:31, 7 February 2024

OCA — Wed, 07 Feb 2024 06:31:45 GMT

←Older revision		Revision as of 06:31, 7 February 2024
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	<StructureSection load='1am2' size='340' side='right'caption='[[1am2]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1am2' size='340' side='right'caption='[[1am2]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1am2]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"mycobacterium_xenopei"_(sic)_schwabacher_1959 "mycobacterium xenopei" (sic) schwabacher 1959~~]. The November 2010 RCSB PDB [~~http~~://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Inteins'' by David Goodsell is [~~http~~://dx.doi.org/10.2210/rcsb_pdb/mom_2010_11 10.2210/rcsb_pdb/mom_2010_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AM2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1AM2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1am2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_xenopi Mycobacterium xenopi]. The November 2010 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Inteins'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2010_11 10.2210/rcsb_pdb/mom_2010_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AM2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AM2 FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>RTP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1789~~ "~~Mycobacterium xenopei~~" ~~(sic) Schwabacher 1959~~])</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.2Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1am2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1am2 OCA], [~~http~~://pdbe.org/1am2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1am2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1am2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1am2 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1am2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1am2 OCA], [https://pdbe.org/1am2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1am2 RCSB], [https://www.ebi.ac.uk/pdbsum/1am2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1am2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GYRA_MYCXE GYRA_MYCXE]] DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings (By similarity).	+	[https://www.uniprot.org/uniprot/GYRA_MYCXE GYRA_MYCXE] DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 19:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1am2 ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1am2 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Several genes from prokaryotes and lower eukaryotes have been found to contain an in-frame open reading frame, which encodes for an internal protein (intein). Post-translationally, the internal polypeptide auto-splices and ligates the external sequences to yield a functional external protein (extein) and an intein. Most, but not all inteins, contain, apart from a splicing domain, a separate endonucleolytic domain that enables them to maintain their presence by a homing mechanism. We report here the crystal structure of an intein found in the gyrase A subunit from Mycobacterium xenopi at 2.2 A resolution. The structure contains an unusual beta-fold with the catalytic splice junctions at the ends of two adjacent antiparallel beta-strands. The arrangement of the active site residues Ser 1, Thr 72, His 75, His 197, and Asn 198 is consistent with a four-step mechanism for the cleavage-ligation reaction. Using site-directed mutagenesis, the N-terminal cysteine, proposed as the nucleophile in the first step of the splicing reaction, was changed to a Ser 1 and Ala 0, thus capturing the intein in a pre-spliced state.
-
-	Crystal structure of GyrA intein from Mycobacterium xenopi reveals structural basis of protein splicing.,Klabunde T, Sharma S, Telenti A, Jacobs WR Jr, Sacchettini JC Nat Struct Biol. 1998 Jan;5(1):31-6. PMID:9437427<ref>PMID:9437427</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1am2" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Inteins]]		[[Category: Inteins]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Mycobacterium xenopi]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
-	[[Category: Klabunde, T]]	+	[[Category: Klabunde T]]
-	[[Category: Sacchettini~~, J C~~]]	+	[[Category: Sacchettini JC]]
-	[[Category: Sharma, S]]	+	[[Category: Sharma S]]
-	~~[[Category: Intein]]~~	+
-	~~[[Category: Protein splicing~~]]	+

OCA at 10:10, 18 November 2020

OCA — Wed, 18 Nov 2020 10:10:08 GMT

←Older revision		Revision as of 10:10, 18 November 2020
Line 1:		Line 1:

	==GYRA INTEIN FROM MYCOBACTERIUM XENOPI==		==GYRA INTEIN FROM MYCOBACTERIUM XENOPI==
-	<StructureSection load='1am2' size='340' side='right' caption='[[1am2]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='1am2' size='340' side='right'caption='[[1am2]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1am2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"mycobacterium_xenopei"_(sic)_schwabacher_1959 "mycobacterium xenopei" (sic) schwabacher 1959]. The November 2010 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Inteins'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2010_11 10.2210/rcsb_pdb/mom_2010_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AM2 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1AM2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1am2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"mycobacterium_xenopei"_(sic)_schwabacher_1959 "mycobacterium xenopei" (sic) schwabacher 1959]. The November 2010 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Inteins'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2010_11 10.2210/rcsb_pdb/mom_2010_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AM2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1AM2 FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RTP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1789 "Mycobacterium xenopei" (sic) Schwabacher 1959])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RTP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1789 "Mycobacterium xenopei" (sic) Schwabacher 1959])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1am2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1am2 OCA], [http://pdbe.org/1am2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1am2 RCSB], [http://www.ebi.ac.uk/pdbsum/1am2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1am2 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1am2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1am2 OCA], [http://pdbe.org/1am2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1am2 RCSB], [http://www.ebi.ac.uk/pdbsum/1am2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1am2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/am/1am2_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/am/1am2_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Inteins]]		[[Category: Inteins]]
		+	[[Category: Large Structures]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Klabunde, T]]		[[Category: Klabunde, T]]

OCA at 10:46, 15 November 2017

OCA — Wed, 15 Nov 2017 10:46:56 GMT

←Older revision		Revision as of 10:46, 15 November 2017
Line 1:		Line 1:
		+
	==GYRA INTEIN FROM MYCOBACTERIUM XENOPI==		==GYRA INTEIN FROM MYCOBACTERIUM XENOPI==
	<StructureSection load='1am2' size='340' side='right' caption='[[1am2]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1am2' size='340' side='right' caption='[[1am2]], [[Resolution\|resolution]] 2.20Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1am2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"mycobacterium_xenopei"_(sic)_schwabacher_1959 "mycobacterium xenopei" (sic) schwabacher 1959]. The November 2010 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Inteins'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2010_11 10.2210/rcsb_pdb/mom_2010_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AM2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AM2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1am2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"mycobacterium_xenopei"_(sic)_schwabacher_1959 "mycobacterium xenopei" (sic) schwabacher 1959]. The November 2010 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Inteins'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2010_11 10.2210/rcsb_pdb/mom_2010_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AM2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AM2 FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RTP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1789 "Mycobacterium xenopei" (sic) Schwabacher 1959])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RTP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1789 "Mycobacterium xenopei" (sic) Schwabacher 1959])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1am2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1am2 OCA], [http://pdbe.org/1am2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1am2 RCSB], [http://www.ebi.ac.uk/pdbsum/1am2 PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1am2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1am2 OCA], [http://pdbe.org/1am2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1am2 RCSB], [http://www.ebi.ac.uk/pdbsum/1am2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1am2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	[[Category: Sharma, S]]		[[Category: Sharma, S]]
	[[Category: Intein]]		[[Category: Intein]]
		+	[[Category: Protein splicing]]

OCA at 08:34, 8 February 2016

OCA — Mon, 08 Feb 2016 08:34:54 GMT

←Older revision		Revision as of 08:34, 8 February 2016
Line 16:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1am2 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:46, 10 September 2015

OCA — Thu, 10 Sep 2015 09:46:11 GMT

←Older revision		Revision as of 09:46, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1am2' size='340' side='right' caption='[[1am2]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1am2' size='340' side='right' caption='[[1am2]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1am2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mycobacterium_xenopi Mycobacterium xenopi~~]. The November 2010 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Inteins'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2010_11 10.2210/rcsb_pdb/mom_2010_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AM2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AM2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1am2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"mycobacterium_xenopei"_(sic)_schwabacher_1959 "mycobacterium xenopei" (sic) schwabacher 1959]. The November 2010 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Inteins'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2010_11 10.2210/rcsb_pdb/mom_2010_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AM2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AM2 FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RTP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1789 Mycobacterium ~~xenopi~~])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RTP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1789 "Mycobacterium xenopei" (sic) Schwabacher 1959])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1am2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1am2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1am2 RCSB], [http://www.ebi.ac.uk/pdbsum/1am2 PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1am2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1am2 OCA], [http://pdbe.org/1am2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1am2 RCSB], [http://www.ebi.ac.uk/pdbsum/1am2 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 26:		Line 26:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1am2" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 31:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Inteins]]		[[Category: Inteins]]
-	[[Category: Mycobacterium xenopi]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Klabunde, T]]		[[Category: Klabunde, T]]

OCA at 22:00, 24 December 2014

OCA — Wed, 24 Dec 2014 22:00:40 GMT

←Older revision		Revision as of 22:00, 24 December 2014
Line 6:		Line 6:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1am2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1am2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1am2 RCSB], [http://www.ebi.ac.uk/pdbsum/1am2 PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1am2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1am2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1am2 RCSB], [http://www.ebi.ac.uk/pdbsum/1am2 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GYRA_MYCXE GYRA_MYCXE]] DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 12:07, 22 December 2014

OCA — Mon, 22 Dec 2014 12:07:22 GMT

←Older revision		Revision as of 12:07, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1am2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_xenopi Mycobacterium xenopi]. The November 2010 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Inteins'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2010_11 10.2210/rcsb_pdb/mom_2010_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AM2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AM2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1am2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_xenopi Mycobacterium xenopi]. The November 2010 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Inteins'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2010_11 10.2210/rcsb_pdb/mom_2010_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AM2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AM2 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RTP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1789 Mycobacterium xenopi])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RTP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1789 Mycobacterium xenopi])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1am2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1am2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1am2 RCSB], [http://www.ebi.ac.uk/pdbsum/1am2 PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1am2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1am2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1am2 RCSB], [http://www.ebi.ac.uk/pdbsum/1am2 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:
	[[Category: Mycobacterium xenopi]]		[[Category: Mycobacterium xenopi]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
-	[[Category: Klabunde, T.]]	+	[[Category: Klabunde, T]]
-	[[Category: Sacchettini, J C.]]	+	[[Category: Sacchettini, J C]]
-	[[Category: Sharma, S.]]	+	[[Category: Sharma, S]]
	[[Category: Intein]]		[[Category: Intein]]

OCA at 08:14, 30 July 2014

OCA — Wed, 30 Jul 2014 08:14:59 GMT

←Older revision		Revision as of 08:14, 30 July 2014
Line 1:		Line 1:
-	[[~~Image~~:1am2.~~png\|left~~\|200px]]	+	==GYRA INTEIN FROM MYCOBACTERIUM XENOPI==
		+	<StructureSection load='1am2' size='340' side='right' caption='[[1am2]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1am2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_xenopi Mycobacterium xenopi]. The November 2010 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Inteins'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2010_11 10.2210/rcsb_pdb/mom_2010_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AM2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AM2 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RTP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1789 Mycobacterium xenopi])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1am2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1am2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1am2 RCSB], [http://www.ebi.ac.uk/pdbsum/1am2 PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/am/1am2_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Several genes from prokaryotes and lower eukaryotes have been found to contain an in-frame open reading frame, which encodes for an internal protein (intein). Post-translationally, the internal polypeptide auto-splices and ligates the external sequences to yield a functional external protein (extein) and an intein. Most, but not all inteins, contain, apart from a splicing domain, a separate endonucleolytic domain that enables them to maintain their presence by a homing mechanism. We report here the crystal structure of an intein found in the gyrase A subunit from Mycobacterium xenopi at 2.2 A resolution. The structure contains an unusual beta-fold with the catalytic splice junctions at the ends of two adjacent antiparallel beta-strands. The arrangement of the active site residues Ser 1, Thr 72, His 75, His 197, and Asn 198 is consistent with a four-step mechanism for the cleavage-ligation reaction. Using site-directed mutagenesis, the N-terminal cysteine, proposed as the nucleophile in the first step of the splicing reaction, was changed to a Ser 1 and Ala 0, thus capturing the intein in a pre-spliced state.

-	~~{{STRUCTURE_1am2\| PDB=1am2 \| SCENE= }}~~	+	Crystal structure of GyrA intein from Mycobacterium xenopi reveals structural basis of protein splicing.,Klabunde T, Sharma S, Telenti A, Jacobs WR Jr, Sacchettini JC Nat Struct Biol. 1998 Jan;5(1):31-6. PMID:9437427<ref>PMID:9437427</ref>

-	~~===GYRA INTEIN FROM MYCOBACTERIUM XENOPI===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_9437427}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1am2]] is~~ a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_xenopi Mycobacterium xenopi]. The November 2010 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the ~~Month] feature on ''Inteins'' by David Goodsell is [http://dx~~.~~doi~~.~~org/10~~.~~2210~~/~~rcsb_pdb/mom_2010_11 10.2210/rcsb_pdb/mom_2010_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AM2 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:009437427<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Inteins]]		[[Category: Inteins]]
	[[Category: Mycobacterium xenopi]]		[[Category: Mycobacterium xenopi]]

OCA: Protected "1am2" [edit=sysop:move=sysop]

OCA — Sun, 21 Oct 2012 12:20:00 GMT

Protected "1am2" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:20, 21 October 2012

OCA at 12:19, 21 October 2012

OCA — Sun, 21 Oct 2012 12:19:57 GMT

←Older revision		Revision as of 12:19, 21 October 2012
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-	{{Seed}}
	[[Image:1am2.png\|left\|200px]]		[[Image:1am2.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1am2", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1am2\| PDB=1am2 \| SCENE= }}		{{STRUCTURE_1am2\| PDB=1am2 \| SCENE= }}

	===GYRA INTEIN FROM MYCOBACTERIUM XENOPI===		===GYRA INTEIN FROM MYCOBACTERIUM XENOPI===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_9437427}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 9437427 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_9437427}}		{{ABSTRACT_PUBMED_9437427}}

	==About this Structure==		==About this Structure==
-	~~1AM2~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_xenopi Mycobacterium xenopi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AM2 OCA].	+	[[1am2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_xenopi Mycobacterium xenopi]. The November 2010 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Inteins'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2010_11 10.2210/rcsb_pdb/mom_2010_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AM2 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~9437427~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:009437427</ref><references group="xtra"/>
		+	[[Category: Inteins]]
	[[Category: Mycobacterium xenopi]]		[[Category: Mycobacterium xenopi]]
		+	[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Klabunde, T.]]		[[Category: Klabunde, T.]]
	[[Category: Sacchettini, J C.]]		[[Category: Sacchettini, J C.]]
	[[Category: Sharma, S.]]		[[Category: Sharma, S.]]
	[[Category: Intein]]		[[Category: Intein]]
-	[[Category: Protein splicing]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 20:38:40 2009''